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In short, it can be tricky. The only opco I'm aware of that has an official policy on it is East Coast, where you basically need two people travelling, each of them with a prereserved bike slot.
When we went out to Maldon, we picked that line because we thought there would be a big guard van on the train, as there had been when we'd taken bikes out that way previously. But there wasn't, so we were reliant on the goodwill / inattentiveness of station and train staff. I imagine the law of averages means that this strategy could bite you at some point.
Nick - there's a lovely short wheelbase Bob Jackson on the 'bay currently!
How was it getting the tandem on a train?
Also I'm very jealous of such outings as this, a tandem is top of the list when we have more space.